Freesurfer August 2004

freesurfer@nmr.mgh.harvard.edu

20 participants
30 discussions

QA and documentation
by Bruce Fischl 12 Aug '04

12 Aug '04

Hi All, I have a favor to ask. We are trying to generate funding to hire a person to do quality assurance, and another to generate documentation, but it has been difficult. We are currently writing a grant explicitly for these positions, and one of the requirements of the funding mechanism is to show that there is a community that would benefit from the proposed resource. That said, it would be a huge help if as many people who use freesurfer as possible would send me letters of support indicating how having such people to work on these things would help their research. Even better, if the research is NIH funded and you could indicate tthe grant that would benefit. I'll append my mailing address. I you are interested, send me email, and I'll send you the offical title of the grant when we finalize it. This will probably be the most boring grant ever written, and I think the only possibility we have for getting it funded is to really document the extensive need for such positions, which I think are absolutely critical as the software has increased in complexity. We know there are bugs in it, it's just a question of putting the effort into finding them :). thanks, Bruce -------------------------------------------------------- Bruce Fischl email: fischl(a)nmr.mgh.harvard.edu Mass. General Hosp. NMR Center. tel:(617)-726-4897 Rm. 2301, Building 149, 13th Street fax:(617)-726-7422 Charlestown, MA 02129 USA

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overview of motion correction
by Chekema Nayasha Prince 12 Aug '04

12 Aug '04

I would like to take 3 different scan volumes of the same subject and compare their parcellation values. I want to make sure that motion between the scans will not change the parcellation values. Is mri_motion_correct the proper tool to use for aligning the scans before proceeding with the processing stream? -Keyma

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mri_motion_correct
by Chekema Nayasha Prince 11 Aug '04

11 Aug '04

Can you use mri_motion_correct to align orig volumes from 2 different scans without averaging the volumes in the output? -Keyma

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Viewing FEAT statistics on Freesurfer surface
by Yung Lyou 06 Aug '04

06 Aug '04

hi, I have been using the FSL&Freesurfer interoperation webpage http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html as a guide to overlay the functional data processed using FSL. When I try to view the FEAT statistics on the surfrace using tksurfer by calling the script "qsurfer" i run into a command not identified error. All my efforts to find this command has proven fruitless and I'm starting to think that i must have somehow erased the script or not installed it when I downloaded the Freesurfer package. I was wondering if someone could tell me where this script lives in the Freesurfer package and what it does. thanks, Yung

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Problems with Talaraich Coordinate Generation
by Yung Lyou 06 Aug '04

06 Aug '04

Hi, I've been struggling recently with trying to generate the transform matrix for the Talaraich coordinate data in TkSurfer. I've installed the MNI packages into the directories specified by the installation files. If someone could perhaps shed some light on which files the Freesurfer package utilizes to generate the talaraich transform matrix and which path it is looking for to find these files that'd be great. thanks, Yung Lyou SUNY Upstate Dept. of Neurosurgery

2 1

tkregister2 crashes/core reader?
by Nguyen, Thang Q 05 Aug '04

05 Aug '04

Hello all, I was running tkregister2 and it crashed on me after 2 seconds of being visible. We have Redhat 9.0 and opengl available on the systems and I ran tkregister2 before. Is there a way to read the core file and determine the problem? Thanks, Thang ------------------------ Thang Nguyen Psychiatry and Human Behavior - Brain Imaging Center University of California, Irvine Email: thangqn(a)uci.edu This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

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Tal and RAS coordinates
by Ketwaroo, Gyanprakash Avinash 05 Aug '04

05 Aug '04

Hi, We are doing an ROI analysis of the cingulate region and specifically want to subdivide this area into anterior and posterior as well as dorsal and rostral ACC. Thus far, we have labels depicting the cingulate gyrus and sulcus and methods for division of cingulate into anterior and posterior and rostral and dorsal. However, these divisions are based on coordinates in Tal space. Tksurfer seems to write the coordinates of the label in RAS coordinates. Is there a simple transformation between Tal and RAS space that would facilitate division in the RAS coordinate system? Thanks, Avinash

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mri_normalize error
by Chekema Nayasha Prince 04 Aug '04

04 Aug '04

Hello, I'm trying to normalize an MPRAGE dataset and I received the following message from the mri_normalize: MRInormalize:could not find any valid peaks no such file or directory mri_normalize: normalization failed no such file or directory I tried to set control points ( 4 of them specifically) in the wm and tried to rerun the mri_normalize but I received the same error. my orig volume looks just like my other datasets that worked properly. Can you let me know what could be causing the error? -Keyma

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Importing FSL to Freesurfer
by Yung Lyou 03 Aug '04

03 Aug '04

Hi, My name is Yung at SUNY upstate and i've been trying to interoperate Freesurfer & FSL. I am currently having problems with the second step of "displaying FEAT statistics on Surface" (http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) posted online. The creation of a registration transform is giving me the following errors. If i enter in the following command tkregister2 --s <subjid> --mov <functional image.img> \ --fslreg <transform martix.mat> --reg func2struc.dat --noedit the error ERROR: SUBJECTS_DIR undefined. Use setenv or -sd and when i try to enter an additional "--sd" argument the error ERROR: cannot determine type of <subject dir> occurs. I was wondering if perhaps anyone would be kind enough to lend a hand. thanks, yung

2 1

SaveSegmentation problem fixed in tkmedit
by Kevin Teich 02 Aug '04

02 Aug '04

I finally found the source of the SaveSegmentation error many of you have been getting. Download this file: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/tkmedit.tcl Move it to this location: $FREESURFER_HOME/lib/tcl/tkmedit.tcl You can overwrite the existing file. -- Kevin Teich

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Freesurfer August 2004